N - mixture models by species

modelling N by site to get relative abundance

abundance by site will be used as a cov on predator occupancy

7 models evaluated, dot, jdt + jdtSQ, lure + jdt + jdtSQ


Species:      BeldingsGroundSquirrel



Metadata Summary:

N_sites N_counts N_detections rep_period iterations burnin thin
127 437 72 7 days 120000 20000 10



Detections by Year:

Yr 2016 2017 2018 2019 2020
sites 19 31 19 32 26
detections 10 56 3 0 3
N.dot.model 5 16 2 0 2



WAIC

Models by WAIC:
model description WAIC N.total.est
fm7 counts 13.94475 54
fm5 jdt + jdtSq 315.37097 39
fm6 lure + jdt + jdtSq 316.37138 39
fm2 jdt 324.57210 38
fm4 lure + jdt 326.28625 39
fm1 dot 423.41197 25
fm3 lure 427.11536 30



Model summaries:



model: fm1
dot



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
p[1] NA 6209 0.097 0.084 0.04 0.16 0 1.0008
p[2] NA 5130 0.130 0.129 0.09 0.17 0 1.001
p[3] NA 4800 0.039 0.023 0.00 0.07 0 0.994
p[4] NA 9978 0.483 0.142 0.00 0.88 0 0.9829
p[5] NA 4589 0.034 0.021 0.00 0.06 0 0.9931
lambda[1] NA 3566 0.318 0.221 0.07 0.54 0 1.0006
lambda[2] NA 6793 0.637 0.583 0.33 0.92 0 1.001
lambda[3] NA 1613 0.224 0.068 0.00 0.41 0 0.9871
lambda[4] NA 7897 0.000 err 0.00 0.00 err err
lambda[5] NA 1599 0.201 0.057 0.00 0.39 0 0.988
N[68] NA 2494 0.112 err 0.00 0.00 err err
N[119] NA 3596 0.144 err 0.00 1.00 err err
N[37] NA 8671 1.055 err 1.00 1.00 err err
N[9] NA 4296 0.072 err 0.00 0.00 err err
N[81] NA 0 0.000 err 0.00 0.00 err err

p[1]

p[2]

p[3]

p[4]

p[5]

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[68]

N[119]

N[37]

N[9]

N[81]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).







model: fm2
jdt



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha jdt 2005 2.069 2.075 1.60 2.51 0 1.001
alpha0 NA 1890 -3.991 -3.949 -4.54 -3.38 0 1.001
lambda[1] NA 8461 0.326 0.23 0.08 0.54 0 1.0008
lambda[2] NA 8231 0.969 0.866 0.55 1.37 0 1.001
lambda[3] NA 9042 0.145 0.076 0.00 0.28 0 0.9939
lambda[4] NA 10000 0.000 err 0.00 0.00 err err
lambda[5] NA 10000 0.116 0.05 0.01 0.22 0 0.9939
N[38] NA 9522 0.913 0 0.00 2.00 1 err
N[68] NA 7712 0.034 err 0.00 0.00 err err
N[16] NA 9610 0.075 err 0.00 0.00 err err
N[91] NA 0 0.000 err 0.00 0.00 err err
N[15] NA 10000 0.056 err 0.00 0.00 err err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[38]

N[68]

N[16]

N[91]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[15]

alpha relationship







model: fm3
lure



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha lure 9106 0.179 0.196 -0.04 0.41 0.42161 0.8983
alpha0 NA 4026 -2.477 -2.423 -2.83 -2.12 0 1.001
lambda[1] NA 8326 0.346 0.255 0.09 0.58 0 1.0008
lambda[2] NA 5292 0.986 0.908 0.52 1.41 0 1.001
lambda[3] NA 10000 0.116 0.056 0.01 0.22 0 0.9939
lambda[4] NA 10000 0.000 err 0.00 0.00 err err
lambda[5] NA 10000 0.091 0.046 0.00 0.17 0 0.9935
N[55] NA 10000 0.005 err 0.00 0.00 err err
N[68] NA 9844 0.008 err 0.00 0.00 err err
N[106] NA 10000 0.065 err 0.00 0.00 err err
N[50] NA 8965 0.043 err 0.00 0.00 err err
N[116] NA 9698 0.032 err 0.00 0.00 err err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[55]

N[68]

N[106]

N[50]

N[116]

alpha relationship







model: fm4
lure + jdt



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha[1] lureDays 6764 -0.074 -0.096 -0.34 0.20 0.85684 0.6755
alpha[2] julianDt 2000 2.073 2.051 1.62 2.50 0 1.001
alpha0 NA 1764 -4.019 -3.977 -4.60 -3.44 0 1.001
lambda[1] NA 8807 0.323 0.236 0.08 0.55 0 1.0009
lambda[2] NA 8112 0.987 0.95 0.55 1.39 0 1.001
lambda[3] NA 10000 0.146 0.065 0.00 0.28 0 0.9938
lambda[4] NA 10000 0.000 err 0.00 0.00 err err
lambda[5] NA 8183 0.130 0.054 0.00 0.25 0 0.9936
N[81] NA 0 0.000 err 0.00 0.00 err err
N[59] NA 9292 0.037 err 0.00 0.00 err err
N[30] NA 10000 1.036 err 1.00 1.00 err err
N[56] NA 10000 0.032 err 0.00 0.00 err err
N[13] NA 9707 1.053 err 1.00 1.00 err err

alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[81]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[59]

N[30]

N[56]

N[13]







model: fm5
jdt + jdtSq



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha[1] julianDt 66 5.611 5.04 3.25 8.22 0 1.001
alpha[2] julianDtSq 72 -1.779 -1.598 -2.92 -0.66 0.02373 0.9992
alpha0 NA 73 -5.853 -5.551 -7.37 -4.24 0 1.001
lambda[1] NA 9585 0.313 0.241 0.08 0.53 0 1.0008
lambda[2] NA 6519 1.067 0.95 0.58 1.54 0 1.001
lambda[3] NA 10238 0.142 0.076 0.00 0.27 0 0.9927
lambda[4] NA 10000 0.000 err 0.00 0.00 err err
lambda[5] NA 9414 0.114 0.063 0.00 0.22 0 0.9934
N[125] NA 10595 0.114 err 0.00 0.00 err err
N[72] NA 0 0.000 err 0.00 0.00 err err
N[127] NA 10000 0.035 err 0.00 0.00 err err
N[4] NA 10291 1.056 err 1.00 1.00 err err
N[93] NA 0 0.000 err 0.00 0.00 err err

alpha[1]

alpha[2]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[125]

N[72]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[127]

N[4]

N[93]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

julian date relationship







model: fm6
lure + jdt + jdtSq



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha[1] lureDays 5902 -0.023 -0.026 -0.30 0.24 0.98436 0.5595
alpha[2] julianDt 96 5.479 5.022 3.34 7.72 0 1.001
alpha[3] julianDtSq 106 -1.715 -1.595 -2.70 -0.69 0.0067 1.0002
alpha0 NA 101 -5.785 -5.712 -7.16 -4.43 0 1.001
lambda[1] NA 8592 0.311 0.229 0.08 0.52 0 1.0009
lambda[2] NA 6730 1.064 0.944 0.58 1.52 0 1.001
lambda[3] NA 9665 0.144 0.066 0.01 0.28 0 0.9935
lambda[4] NA 10000 0.000 err 0.00 0.00 err err
lambda[5] NA 7892 0.121 0.056 0.01 0.23 0 0.9937
N[118] NA 8579 0.032 err 0.00 0.00 err err
N[97] NA 0 0.000 err 0.00 0.00 err err
N[40] NA 8481 0.100 err 0.00 0.00 err err
N[36] NA 9554 1.166 err 1.00 2.00 err err
N[69] NA 10000 0.033 err 0.00 0.00 err err

alpha[1]

alpha[2]

alpha[3]

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[118]

N[97]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[40]

N[36]

N[69]







model: fm7
counts



summary table

param covariate iters_ef mean mode hdi_89pct_lower hdi_89pct_upper bayes_P pct.density
alpha counts 7690 13.312 13.448 11.04 15.57 0 1.001
alpha0 NA 6710 -5.721 -5.525 -6.71 -4.67 0 1.001
lambda[1] NA 7367 0.916 0.667 0.24 1.59 0 1.0007
lambda[2] NA 9657 0.984 0.933 0.55 1.39 0 1.001
lambda[3] NA 4586 0.765 0.367 0.04 1.47 0 0.9928
lambda[4] NA 4640 0.000 err 0.00 0.00 err err
lambda[5] NA 3342 0.737 0.396 0.04 1.43 0 0.9921
N[54] NA 7143 0.738 0 0.00 2.00 1 err
N[89] NA 10000 0.000 err 0.00 0.00 err err
N[97] NA 10000 0.000 err 0.00 0.00 err err
N[22] NA 0 1.000 err 1.00 1.00 err err
N[60] NA 7190 0.727 0 0.00 2.00 1 err

alpha

alpha0

lambda[1]

lambda[2]

lambda[3]

lambda[4]

lambda[5]

N[54]

N[89]

N[97]

N[22]

## Warning in cor(X, use = "pairwise.complete.obs"): the standard deviation is zero
## Warning: Removed 50 rows containing missing values (geom_bar).

N[60]

alpha relationship